Generation of High-Quality African Swine Fever Virus Complete Genome from Field Samples by Next-Generation Sequencing.

African swine fever (ASF) is a lethal contagious viral disease of domestic pigs and wild boars caused by the African swine fever virus (ASFV). The pandemic spread of ASF has caused severe effects on the global pig industry. Whole-genome sequencing provides crucial information for virus strain characterization, epidemiology analysis and vaccine development. Here, we evaluated the performance of next-generation sequencing (NGS) in generating ASFV genome sequences from clinical samples. Thirty-four ASFV-positive field samples including spleen, lymph node, lung, liver and blood with a range of Ct values from 14.73 to 25.95 were sequenced. For different tissue samples collected from the same sick pigs, the proportion of ASFV reads obtained from the spleen samples was 3.69-9.86 times higher than other tissues. For the high-viral-load spleen samples (Ct < 20), a minimum of a 99.8% breadth of ≥10× coverage was revealed for all the samples. For the spleen samples with Ct ≥ 20, 6/12 samples had a minimum of a 99.8% breadth of ≥10× coverage. A high average depth of sequencing coverage was also achieved from the blood samples. According to our results, high-quality ASFV whole-genome sequences could be obtained from the spleen or blood samples with Ct < 20. The high-quality ASFV genome sequence generated in this study was further used for the high-resolution phylogenetic analysis of the ASFV genomes in the early stage of the ASF epidemic in China. Our study demonstrates that NGS may act as a useful tool for efficient ASFV genome characterization, providing valuable information for disease control.

Continuous surveillance revealing a wide distribution of class I Newcastle disease viruses in China from 2011 to 2020.

The risk-based active surveillance for Newcastle disease virus (NDV) was carried out in China from 2011 to 2020. A total of 110,018 swabs were collected from 28 provinces. 2,389 class I NDVs were isolated and identified by RT-PCR and sequencing. The average annual positivity rate of class I NDVs from 2011 to 2020 was 2.17%. In the last 10 years, the positivity rate was highest in 2011 (4.76%), and has since decreased. Most viruses were isolated from chickens, while others were collected from ducks, geese and pigeons, as well as from the environment. The positivity rates for class I NDVs in poultry ranged from 0.55% to 2.40%. The viruses were isolated from 373 sampling sites in 24 provinces, mainly in East, Central, South and Southwest China. The positivity rates of NDVs in wholesale markets (51.58%) and retail markets (42.83%) were much higher than those in poultry farms (7.14%) and slaughterhouses (3.85%). Phylogenetic analyses showed that most isolates belonged to sub-genotype 1.1.2, while only 22 viruses belonged to sub-genotype 1.2, indicating the viruses in sub-genotype 1.1.2 were the predominant strains in China. The F and HN genes of six strains in the two sub-genotypes were sequenced and analyzed. The cleavage sites of F protein in the six viruses were 112ERQER/L117, 112ERQGR/L117 or 112GRQERL117, which were typical of low virulence NDV. Several mutations were identified in the functional domains of F and HN proteins, including fusion peptide, heptad repeat region, transmembrane domains and neutralizing epitopes. This study revealed the distribution, genetic and phylogenetic characteristics of class I NDVs in China, and could help us to better understand the epidemiological context of class I NDVs in China.

Observation of intermediates by online mass spectrometry to demonstrate the multiple mechanisms of dye-sensitized photocatalysis.

Online mass spectrometry was applied to reveal multiple mechanisms of visible-light irradiated dye-sensitized photocatalysis for o-phenylenediamine oxidation. The reactants, products and short-lived intermediates were recorded and dynamically tracked. Dimer and unexpected trimer intermediates were observed to deduce the stepwise aerobic photooxidation mechanism with multiple routes, which was supported by theoretical calculations.

Comparison between class I NDV and class II NDV in aerosol transmission under experimental condition.

Recent epidemiological surveys have shown that class I Newcastle disease virus (NDV) is widely distributed in China. However, little is currently known about its transmission. Therefore, in this study, we compared the transmission of class I and class II NDV. Specific-pathogen-free chickens were divided into a class I NDV inoculation group and an aerosol-exposed infection group and kept in 2 separate isolators (A and B, respectively) that were connected with an airtight plastic pipe. After inoculation, air samples were collected regularly with an All-Glass Impinger-30 (Liaoyang, China), and the airborne virus contents were analyzed using the plaque count method. In addition, oral and cloacal swabs were collected regularly to detect virus shedding using quantitative reverse transcription PCR. Similar trials were conducted simultaneously with class II NDV in isolators C and D. We consistently detected class I NDV aerosols in both isolators A and B up to 40 D post-inoculation (dpi). The aerosol concentration reached a maximum of 13.81 × 103 plague-forming units per cubic meter of air at 18 dpi and was significantly higher than that of class II NDV at 21 and 24 dpi. We also detected class I virus shedding from 2 to 40 dpi in the inoculated chickens and from 7 to 40 D post-aerosol-exposed infection in the aerosol-exposed chickens. This phenomenon may explain why class I NDV has been the primary epidemic strain of NDV in recent years.

Molecular characterization of new emerging sub-genotype VIIh Newcastle disease viruses in China.

Newcastle disease (ND) has been enzootic in China for several decades since the first recognition of the disease in 1946 in China. Continuous surveillance revealed that the sub-genotype VIId Newcastle disease virus (NDV) has been predominantly responsible for most of ND outbreak in China in recent years. But in the present study, three virulent NDVs isolated from poultry in southern China were classified as sub-genotype VIIh, which is highly related to the viruses circulating in some Southeast Asia countries. Continuous isolation of genotype VIIh NDV strains in the region suggests its panzootic potential. This is the first report of the sub-genotype VIIh NDVs in domestic poultry in China. The complete genome length of the three isolates was 15,192 nucleotides, and the motif at the cleavage site of F protein was 112RRRRR/F117 or 112RRRKR/F117, which was typical of virulent NDV. Phylogenetic analysis based on the F gene revealed that the three viruses had close relationship with the sub-genotype VIIh virus isolated from wild bird in 2011 in China. These viruses might have formed a stable lineage in poultry during 2012-2016 and have the potential to cause enzootic in China. Our study revealed the genetic and phylogenetic characteristics of the three sub-genotype VIIh isolates, which could help us to better understand the epidemiological context of these viruses.

Development of a series of novel 4-anlinoquinazoline derivatives possessing quinazoline skeleton: Design, synthesis, EGFR kinase inhibitory efficacy, and evaluation of anticancer activities in vitro.

4-anilinoquinazoline-based derivatives represent an attractive scaffold for small molecular EGFR-TKIs in the field of medicinal chemistry. A series of novel heterocyclic substituted derivatives have been designed, synthesized and evaluated their antitumor bioactivities as potential EGFR-TKIs. Most of the new compounds exhibited certain efficient inhibition potency for proliferation of a panel of five human cancer cells with IC50 values at the low micromolar level, and some of them possessed good broad-spectrum inhibition activities, compared to Gefitinib. Especially, the IC50 values of compound 21 against HepG2, A549, MCF-7, DU145 and SH-SY5Y cells were 4.61, 9.50, 9.80, 6.79 and 7.77 µM, respectively, which were much lower than those of Gefitinb. Furthermore, the highlighting compound 21 demonstrated excellent inhibition activity against EGFR-TK with the IC50 value of 3.62 nM, similar to that of Gefitinib(2.21 nM). The results of LDH release assay proved that compound 21 was anti-proliferative rather than cytotoxicity on HepG2 cells. Compound 21 were able to cause HepG2 cells to block in S phase and induce cell death mainly by apoptosis through a mitochondrial dependent pathway. Moreover, the assessment of MMP, the determination of intracellular free Ca2+ concentration, the production of ROS, and the effects on the activity of caspase-3 in a dose-dependent manner demonstrated that compound 21 induced cell apoptosis in HepG2 cells through the Ca2+/ROS-mediated mitochondria/caspase-dependent apoptosis pathway largely. These preliminary results evidenced that compound 21 could be a potential antitumor agent deserving further study.

(R)- and (S)-18F-labeled 2-arylbenzofurans with improved pharmacokinetics as ß-amyloid imaging probes.

A new class of optical isomers of 2-arylbenzofuran derivatives were synthesized and evaluated as potential ß-amyloid plaques imaging agents. Both lipophilicity and signal-to-noise ratio were significantly improved by adding a chiral hydroxyl group to 1-fluoro-3-(oxidanyl)propan-2-ol side chain. These derivatives displayed moderate to high binding affinity towards Aß1-42 aggregates. Four tracers possessing potent binding affinity (Ki < 30 nM) were chosen for further investigation. In in vitro autoradiography studies, the four selected probes showed effective binding to Aß plaques in Tg mouse and AD human brain tissue after labeled by 18F. The purified enantiomers displayed apparent discrepancy in biodistribution experiments in normal mice, for (S)-enantiomers provided rather faster clearance than (R)-enantiomers. All in all, (S)-[18F]17 (Ki = 14.6 nM) with excellent pharmacokinetics (brain2 min = 8.60% ID/g, brain2 min/brain60 min = 14.1) deserves further evaluation.

Genomic Characterizations of a Newcastle Disease Virus Isolated from Ducks in Live Bird Markets in China.

One class I Newcastle disease virus (NDV), designated as duck/Guangxi/1261/2015 (GX1261), was isolated from asymptomatic ducks in live bird markets (LBM) from southern China during the national active surveillance for NDVs in 2015. The complete genome length of GX1261 isolate was 15,198 nucleotides with the gene order of 3'-NP-P-M-F-HN-L-5'. The motif at the cleavage site of F protein was 112ERQER/L117, which was typical of low virulence NDV. Several mutations were identified in the functional domains of F and HN proteins, including fusion peptide, heptad repeat region, transmembrane domains and neutralizing epitopes. Phylogenetic analysis based on the complete F gene revealed that the isolate was clustered into sub-genotype 1c in class I, and showed a high level of similarity with the strains isolated from waterfowl in the United States of America. This is the first report of this kind of virus in the mainland of China. These results demonstrated that GX1261-like viruses might exist in asymptomatic waterfowl, and remain undetected or unidentified. Thus, more investigation needs to be done in order to identify the source of the virus. This study revealed the genetic and phylogenetic characteristics of GX1261 isolate and could help us to better understand the epidemiological context of class I NDV in China.

In-situ nanoelectrospray for high-throughput screening of enzymes and real-time monitoring of reactions.

The in-situ and high-throughput evaluation of enzymes and real-time monitoring of enzyme catalyzed reactions in liquid phase is quite significant in the catalysis industry. In-situ nanoelectrospray, the direct sampling and ionization method for mass spectrometry, has been applied for high-throughput evaluation of enzymes, as well as the on-line monitoring of reactions. Simply inserting a capillary into a liquid system with high-voltage applied, analytes in liquid reaction system can be directly ionized at the capillary tip with small volume consumption. With no sample pre-treatment or injection procedure, different analytes such as saccharides, amino acids, alkaloids, peptides and proteins can be rapidly and directly extracted from liquid phase and ionized at the capillary tip. Taking irreversible transesterification reaction of vinyl acetate and ethanol as an example, this technique has been used for the high-throughput evaluation of enzymes, fast optimizations, as well as real-time monitoring of reaction catalyzed by different enzymes. In addition, it is even softer than traditional electrospray ionization. The present method can also be used for the monitoring of other homogenous and heterogeneous reactions in liquid phases, which will show potentials in the catalysis industry.

Equilibrium State of PAHs in Bottom Sediment-Water-Suspended Sediment System of a Large River Considering Freely Dissolved Concentrations.

In natural waters, the equilibrium state of hydrophobic organic compounds among bottom sediment (BS), suspended sediment (SPS), and water is fundamental to infer their transfer flux and aqueous bioavailability. However, this type of information remains scarce and fragmented. This study systematically evaluated the equilibrium state of polycyclic aromatic hydrocarbons (PAHs) in the Yangtze River. Total and freely dissolved concentrations of the 16 priority PAHs in pore water and overlying water (including surface and near-bottom) of the Yangtze middle reaches were investigated, as were the concentrations of attached PAHs in SPS and BS. Results showed that concentrations of total/freely dissolved PAHs, dissolved organic carbon (DOC), and SPS in surface water were not statistically different from those in near-bottom water, and the DOC-water distribution coefficients of PAHs in pore water were not statistically different from overlying water. However, significant disequilibrium was found at the sediment-water interface; concentrations of total/freely dissolved PAHs in pore water were 1 to 2 orders of magnitude higher than those in overlying water. This study offers a complete analysis of the potential disequilibrium of PAHs in BS-water-SPS system of large rivers and suggests that distribution of hydrophobic organic compounds between BS and overlying water is essential in controlling their equilibrium state in the BS-water-SPS system of natural waters.

Genomic Characterizations of Six Pigeon Paramyxovirus Type 1 Viruses Isolated from Live Bird Markets in China during 2011 to 2013.

The genomes of six pigeon paramyxovirus type 1 (PPMV-1) isolated from symptomless pigeons in live poultry markets during the national active surveillance from 2011 to 2013 were sequenced and analyzed in this study. The complete genome lengths of all isolates were 15,192 nucleotides with the gene order of 3'-NP-P-M-F-HN-L-5'. All isolates had the same motif of 112RRQKRF117 at the cleavage site of the fusion protein, which was typical of velogenic Newcastle disease virus (NDV). Several mutations were identified in the functional domains of F and HN proteins, including fusion peptide, heptad repeat region, transmembrane domains and neutralizing epitopes. Phylogenetic analysis based on sequences of complete genomes and six genes revealed that all isolates belonged to genotype VI in class II, but at least 2 sub-genotypes were identified. Most isolates were placed into sub-genotype VIb with the exception of pi/GX/1015/13, which was classified in sub-genotype VIa. The obvious antigenic difference between PPMV-1 isolates and La Sota strain was found based on the R-value calculated by cross hemagglutination inhibition (HI) assay. These results provided the evidence that PPMV-1 could be detected from healthy pigeons, and our study may be useful in designing vaccines used in pigeon, and developing molecular diagnostic tools to monitor and prevent future PPMV-1 outbreaks.

A study of the geo-herbalism of evodiae fructus based on a flow-injection mass spectrometric fingerprinting method combined with chemometrics.

A flow-injection mass spectrometric (FIMS) fingerprinting method in combination with principal component analysis (PCA) was used to study the geo-herbalism of Evodiae Fructus (EF) samples. Twenty four EF samples from different regions in China were collected and analyzed. The PCA scores plot showed that the samples from Guizhou Province were scattered in different groups, however, most of the samples from other provinces were basically scattered in the same group. Nine characteristic compounds responsible for the classification of the samples were tentatively characterized. These nine compounds might help differentiating EF samples from different regions.

Dual-modal imaging and photodynamic therapy using upconversion nanoparticles for tumor cells.

Here we synthesized silica-coated NaYF4:Yb,Tm@NaGdF4 nanoparticles with hypocrellin photosensitizers covalently incorporated inside the silica shells, combining dual modal imaging and photodynamic therapy (PDT) functions together. Under excitation at 980 nm, the tumor-targeting specificity of the as-prepared nanomaterials efficiently enhanced as folic acid (FA) was conjugated. The internalization of UCNPs@SiO2@hypocrellin A-FA in HeLa cells and HEK-293 cells was observed by confocal microscopy and in vitro magnetic resonance imaging (MRI), which demonstrated that the as-prepared nanocomposites have the ability to target folate receptor (FR) (+) cells. Moreover, magnetic resonance (MR) measurements also demonstrated that the as-prepared nanocomposites could be used as a contrast agent for MRI. All these results showed the feasibility and potential of the as-prepared nanocomposites for simultaneous imaging and PDT application.

[Detection of an NA gene molecular marker in H7N9 subtype avian influenza viruses by pyrosequencing].

This study aimed to establish a method for the detection and identification of H7N9 avian influenza viruses based on the NA gene by pyrosequencing. According to the published NA gene sequences of the avian influenza A (H7N9) virus, a 15-nt deletion was found in the NA gene of H7N9 avian influenza viruses. The 15-nt deletion of the NA gene was targeted as the molecular marker for the rapid detection and identification of H7N9 avian influenza viruses by pyrosequencing. Three H7N9 avian influenza virus isolates underwent pyrosequencing using the same assay, and were proven to have the same 15-nt deletion. Pyrosequencing technology based on the NA gene molecular marker can be used to identify H7N9 avian influenza viruses.

Development and validation of an UPLC-ESI-MS/MS method for determination of dehydroevodiamine, limonin, evodiamine, and rutaecarpine in Evodiae Fructus.

OBJECTIVE: Evodiae Fructus (EF), one of the most widely used traditional Chinese medicines, mainly consists of alkaloids, is widely used for the treatments of headache and gastrointestinal disorders. In this study, a sensitive and reliable UPLC-ESI-MS/MS method was developed for qualitative determination of dehydroevodiamine, limonin, evodiamine, and rutaecarpine. MATERIALS AND METHODS: Chromatographic separations were accomplished on a Phenomenex Kinetex XB-C18 column (2.1 × 150 mm, 1.7 µm) by using a gradient elution profile with a mobile phase consisting of 0.5% formic acid in water (A) and acetonitrile (B). Detection was performed using multiple reactions monitoring mode under ESI in the positive ion mode. RESULTS: The results showed good linearity over the investigated concentration ranges (R (2)>0.9900) for the analytes. The limit of quantitations (LOQs) were 6.88 ng/mL for dehydroevodiamine, 18.6 ng/mL for limonin, 6.24 ng/mL for evodiamine, and 2.56 ng/mL for rutaecarpine, respectively. Intraday and interday precisions (relative standard deviations, %) were <5% and accuracies ranged from 92% to 106%. CONCLUSION: The validated method was successfully applied to assay the contents of the four compounds in EF samples from different regions, with which just 10 min was needed to analyze each sample.

Genome Sequences of an H5N1 Highly Pathogenic Avian Influenza Virus Isolated from Vaccinated Layers in China in 2012.

An H5N1 virus was isolated from vaccinated layers during an outbreak of highly pathogenic avian influenza (HPAI) in Ningxia, China, in 2012. Phylogenetic analysis revealed that the virus is a novel variant in clade 7.2, and the outbreak likely resulted from mutations in the viral hemagglutinin (HA) gene.

Complete genome sequences of new emerging newcastle disease virus strains isolated from china.

Five Newcastle disease virus strains isolated from geese were classified into a new genotype, designated genotype XII. The complete genome sequences of two strains indicated that these viruses were distinct from viruses of genotype VII. More investigations need to be conducted for us to understand the origin of these new strains.

[Establishment of reverse genetics system for class I NDV08-004 strain].

Based on the genomic sequence of NDV08-004 strain (GenBank accession number FJ794269), seven pairs of primers were designed to amplify the genomic fragments by RT-PCR and cloned into pGEM-Teasy vector. The fragments (named A to G) were sub-cloned into transcription vector pOLTV5 according to the universal RE site and the plasmid named NDV08-004-pO which contained the full length cDNA of NDV08-004 strain was constructed. Three helper plasmids (pCI-NP, pCI-P and pCI-L) together with NDV08-004-pO were co-transfected into BSR T7/5 cells, and the transfection supernatant was inoculated into SPF embryonated eggs to rescue the virus. The virus was rescued successfully and identified by HA and RT-PCR and sequencing. The rescue system constructed in this study provided a good foundation for the further related research.

Evaluating viral interference between Influenza virus and Newcastle disease virus using real-time reverse transcription-polymerase chain reaction in chicken eggs.

BACKGROUND: Simultaneous and sequential allantoic cavity inoculations of Specific-pathogen-free (SPF) chicken eggs with Influenza virus (AIV) and Newcastle disease virus (NDV) demonstrated that the interaction of AIV and NDV during co-infection was variable. Our research revisited the replication interference potential of AIV and NDV using real-time reverse transcription-polymerase chain reaction (real-time RT-PCR) for AIV and NDV to specifically detect the viral genomes in mixed infections. RESULTS: Data from this survey showed that when different doses of NDV (Lasota or F48E8) and AIV (F98 or H5N1) were simultaneously inoculated into embryonating chicken eggs (ECE), interference with the growth of NDV occurred, while interference with the growth of AIV did not occur. When equal amount of the two viruses were sequentially employed, the degree of interference was dependent upon the time of superinfection and the virulence of virus. CONCLUSION: AIV have a negative impact on NDV growth if they are inoculated simultaneously or sequentially and that the degree of interference depended upon the quantity and relative virulence of the virus strains used; however, interference with AIV was not observed. Only if NDV were inoculated at an earlier time will NDV able to interfere with the growth of AIV.

Multiplex RT-PCR for rapid detection and differentiation of class I and class II Newcastle disease viruses.

A multiplex RT-PCR was developed for detection and differentiation of class I and class II strains of Newcastle disease virus (NDV). The method was shown to have high specificity and sensitivity. The results obtained from the multiplex RT-PCR for a total of 67 NDV field isolates obtained in 2009 were consistent with those obtained by nucleotide sequencing and phylogenetic analysis. A phylogenetic tree based on the partial sequences of the F gene revealed that the 67 field isolates of NDV could be divided into two classes. Twenty-seven NDV isolates were grouped into class I, and two genotypes were identified. Most of the class I isolates were determined to be of genotype 3, with the exception of isolate NDV09-034, which belonged to genotype 2. Forty class II NDV isolates were divided into three genotypes, namely genotype VII (27 isolates), genotype I (2 isolates) and genotype II (11 isolates). Isolates of genotypes I and II in class II were shown to be related to commercial vaccine strains used commonly in China. All isolates of genotype VII were predicted to be virulent, on the basis of the sequence motif at the cleavage site of the F gene. This genotype has become predominantly responsible for most outbreaks of ND in China in recent years. In conclusion, this multiplex RT-PCR provides a new assay for rapid detection and differentiation of both classes of NDV isolates.